Hi Christian,
interesting information. Will try it if the workaround works for me as well. However, I haven't had the problem for quite some time.
Another thing which you could try is test drive the new Eclipse release Mars. It is still not fully finished (milestone 4) but I have been using it for over two weeks and it feels pretty solid. It would be interesting to know if the problem still exists in the new release. Apparently Mars also contains a couple of performance fixes and feels faster.
I have to add the disclaimer that we don't officially support Mars, yet. I would recommend to use it with a copy of your workspace to prevent any data loss. You can get it here:
Eclipse Mars M4 Packages | Packages
cheers
Thomas